{"id":"https://openalex.org/W4411765603","doi":"https://doi.org/10.1093/bib/bbaf301","title":"DeepExDC interprets genomic compartmentalization changes in single-cell Hi-C data","display_name":"DeepExDC interprets genomic compartmentalization changes in single-cell Hi-C data","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4411765603","doi":"https://doi.org/10.1093/bib/bbaf301","pmid":"https://pubmed.ncbi.nlm.nih.gov/40581982"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf301","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf301","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf301/63617127/bbaf301.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf301/63617127/bbaf301.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078674561","display_name":"Hongqiang Lv","orcid":"https://orcid.org/0000-0001-5061-4762"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongqiang Lyu","raw_affiliation_strings":["School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103196068","display_name":"Pei Cao","orcid":"https://orcid.org/0000-0002-7599-8982"},"institutions":[{"id":"https://openalex.org/I148099405","display_name":"Xi'an University of Architecture and Technology","ror":"https://ror.org/04v2j2k71","country_code":"CN","type":"education","lineage":["https://openalex.org/I148099405"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pei Cao","raw_affiliation_strings":["School of Information and Control Engineering, Xi'an University of Architecture and Technology , No. 13 Yanta Road, Beilin District, Xi'an, Shaanxi 710055 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Control Engineering, Xi'an University of Architecture and Technology , No. 13 Yanta Road, Beilin District, Xi'an, Shaanxi 710055 ,","institution_ids":["https://openalex.org/I148099405"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Wenyao Long","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenyao Long","raw_affiliation_strings":["School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102077295","display_name":"Xiaoran Yin","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131893","display_name":"Second Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/03aq7kf18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210131893"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoran Yin","raw_affiliation_strings":["Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710004 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710004 ,","institution_ids":["https://openalex.org/I4210131893"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051755640","display_name":"Shengjun Xu","orcid":"https://orcid.org/0000-0002-1679-1885"},"institutions":[{"id":"https://openalex.org/I148099405","display_name":"Xi'an University of Architecture and Technology","ror":"https://ror.org/04v2j2k71","country_code":"CN","type":"education","lineage":["https://openalex.org/I148099405"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shengjun Xu","raw_affiliation_strings":["School of Information and Control Engineering, Xi'an University of Architecture and Technology , No. 13 Yanta Road, Beilin District, Xi'an, Shaanxi 710055 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Control Engineering, Xi'an University of Architecture and Technology , No. 13 Yanta Road, Beilin District, Xi'an, Shaanxi 710055 ,","institution_ids":["https://openalex.org/I148099405"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062656355","display_name":"Laiyi Fu","orcid":"https://orcid.org/0000-0001-9086-3982"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Laiyi Fu","raw_affiliation_strings":["School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.9736,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.74931816,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"26","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9955000281333923,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/compartmentalization","display_name":"Compartmentalization (fire protection)","score":0.952027440071106},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.540867030620575},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5312245488166809},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4900554418563843},{"id":"https://openalex.org/keywords/cellular-compartment","display_name":"Cellular compartment","score":0.46990153193473816},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.448234498500824},{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.4315102696418762},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43136826157569885},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.37725430727005005},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.27304786443710327},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1502789855003357},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11223897337913513},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08676710724830627}],"concepts":[{"id":"https://openalex.org/C110455231","wikidata":"https://www.wikidata.org/wiki/Q897788","display_name":"Compartmentalization (fire protection)","level":3,"score":0.952027440071106},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.540867030620575},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5312245488166809},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4900554418563843},{"id":"https://openalex.org/C78885561","wikidata":"https://www.wikidata.org/wiki/Q189055","display_name":"Cellular compartment","level":3,"score":0.46990153193473816},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.448234498500824},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.4315102696418762},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43136826157569885},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.37725430727005005},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.27304786443710327},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1502789855003357},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11223897337913513},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08676710724830627},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf301","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf301","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf301/63617127/bbaf301.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40581982","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40581982","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11013605","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12206447","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf301","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf301","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf301/63617127/bbaf301.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6324912543","display_name":null,"funder_award_id":"xzy012022087","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8147005953","display_name":null,"funder_award_id":"2024JC-YBMS-783","funder_id":"https://openalex.org/F4320324173","funder_display_name":"Natural Science Foundation of Shaanxi Province"}],"funders":[{"id":"https://openalex.org/F4320324173","display_name":"Natural Science Foundation of Shaanxi Province","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411765603.pdf","grobid_xml":"https://content.openalex.org/works/W4411765603.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1896708637","https://openalex.org/W1965863160","https://openalex.org/W1967327758","https://openalex.org/W1968944537","https://openalex.org/W1973062929","https://openalex.org/W1993570130","https://openalex.org/W2017278106","https://openalex.org/W2036663020","https://openalex.org/W2070021921","https://openalex.org/W2073026107","https://openalex.org/W2080477348","https://openalex.org/W2090037139","https://openalex.org/W2097798909","https://openalex.org/W2114104545","https://openalex.org/W2124566253","https://openalex.org/W2128227827","https://openalex.org/W2129305656","https://openalex.org/W2148143831","https://openalex.org/W2157576490","https://openalex.org/W2190545194","https://openalex.org/W2339613031","https://openalex.org/W2582946425","https://openalex.org/W2597274540","https://openalex.org/W2599773520","https://openalex.org/W2731989040","https://openalex.org/W2928665623","https://openalex.org/W2945038365","https://openalex.org/W2948487481","https://openalex.org/W2949773289","https://openalex.org/W2950541340","https://openalex.org/W2951638683","https://openalex.org/W2962862931","https://openalex.org/W2965970564","https://openalex.org/W2971932838","https://openalex.org/W2972380686","https://openalex.org/W2983176933","https://openalex.org/W2987347191","https://openalex.org/W3015686339","https://openalex.org/W3017348419","https://openalex.org/W3080563305","https://openalex.org/W3087339707","https://openalex.org/W3207880742","https://openalex.org/W3217753204","https://openalex.org/W4207056242","https://openalex.org/W4291019397","https://openalex.org/W4309076319","https://openalex.org/W4379600412","https://openalex.org/W4388035146","https://openalex.org/W4389275981","https://openalex.org/W4391041716","https://openalex.org/W4401247162","https://openalex.org/W4403852249","https://openalex.org/W4404662707","https://openalex.org/W4406142139","https://openalex.org/W6925713331"],"related_works":["https://openalex.org/W2062960570","https://openalex.org/W2030773092","https://openalex.org/W2970302272","https://openalex.org/W141631888","https://openalex.org/W4317654036","https://openalex.org/W3177737022","https://openalex.org/W2592230087","https://openalex.org/W1999236976","https://openalex.org/W4223935384","https://openalex.org/W4387603475"],"abstract_inverted_index":{"Single-cell":[0],"Hi-C":[1,67,114],"(scHi-C)":[2],"technology":[3],"enables":[4],"probing":[5],"of":[6,26,39,63,76,102,157,202,221],"higher-order":[7],"chromatin":[8],"structures":[9],"in":[10,86,105,153,211],"individual":[11],"cells.":[12],"It":[13,112,176],"provides":[14],"an":[15,93],"opportunity":[16],"to":[17,35,166,169,199,229],"get":[18],"a":[19,36,54,84,109,207],"deeper":[20],"insight":[21],"into":[22],"genomic":[23,132],"compartmentalization":[24,77,133,158],"changes":[25,78,134,172],"single":[27,203],"cells":[28],"across":[29,135,173],"different":[30,155],"conditions,":[31],"paving":[32],"the":[33,40,60,70,73,80,118,161,181,195,249],"way":[34],"common":[37],"understanding":[38],"interplay":[41],"among":[42],"compartmental":[43],"organization,":[44],"genome":[45],"functions,":[46],"and":[47,126,130,142,160,205,224,234],"cellular":[48],"phenotypes.":[49],"Unfortunately,":[50],"there":[51],"are":[52,164],"only":[53],"few":[55],"methods":[56,193],"currently":[57],"available":[58],"for":[59,99],"differential":[61,100,127,182,225],"analysis":[62,75,101],"A/B":[64,103],"compartments":[65,104,183],"on":[66,108,140],"data":[68,107,145],"at":[69,79,117,194],"bulk":[71,196],"level;":[72],"computational":[74],"single-cell":[81,119],"level":[82],"is":[83,177,219,238],"field":[85],"its":[87],"infancy.":[88],"Herein,":[89],"we":[90,227],"propose":[91],"DeepExDC,":[92],"interpretable":[94],"1D":[95],"convolutional":[96],"neural":[97],"network":[98],"scHi-C":[106,144],"genome-wide":[110],"scale.":[111],"accepts":[113],"contact":[115],"matrices":[116],"level,":[120,197],"runs":[121],"without":[122],"any":[123],"distribution":[124,222],"assumption":[125],"pattern":[128],"limitation,":[129],"interprets":[131],"multiple":[136,212],"conditions.":[137],"The":[138],"results":[139],"simulated":[141],"experimental":[143],"show":[146],"that":[147,180,217,240],"our":[148,241],"DeepExDC":[149,186,218],"has":[150],"higher":[151],"accuracies":[152],"detecting":[154],"types":[156],"changes,":[159],"interpretation":[162],"values":[163],"demonstrated":[165],"be":[167],"able":[168],"reflect":[170],"compartment":[171],"cell":[174],"types.":[175],"also":[178,243],"observed":[179],"given":[184],"by":[185,191],"agree":[187],"well":[188],"with":[189,248],"those":[190],"state-of-the-art":[192],"help":[198],"characterize":[200],"heterogeneity":[201],"cells,":[204],"exhibit":[206],"reasonable":[208],"biological":[209],"relevance":[210],"regards.":[213],"In":[214],"addition,":[215],"considering":[216],"free":[220],"assumptions":[223],"patterns,":[226],"attempted":[228],"transfer":[230],"it":[231,237],"onto":[232],"scRNA-seq":[233],"scATAC-seq":[235],"data;":[236],"interesting":[239],"method":[242],"presents":[244],"considerable":[245],"power":[246],"compared":[247],"competing":[250],"methods.":[251]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
